@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well                   = 1,
    counts                     = [
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u7b8fcf684b/files/bc_sort.csf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u7b8fcf684b/files/bc_sort.csf",
    ],
    feature_reference          = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u7b8fcf62f7/files/feature_reference.frf.bincode",
    chemistry_defs             = {
        "Gene Expression": {
            barcode: [
                {
                    kind:      "gel_bead",
                    length:    16,
                    offset:    0,
                    read_type: "R1",
                    whitelist: {
                        name:                       "3M-february-2018_TRU",
                        part:                       null,
                        slide:                      null,
                        translation:                false,
                        translation_whitelist_path: null,
                    },
                },
            ],
            barcode_extraction: null,
            description:        "Single Cell 3' v3 (polyA)",
            endedness:          "three_prime",
            name:               "SC3Pv3-polyA",
            rna: {
                length:     null,
                min_length: null,
                offset:     0,
                read_type:  "R2",
            },
            rna2:               null,
            strandedness:       "+",
            umi: [
                {
                    length:     12,
                    min_length: 10,
                    offset:     16,
                    read_type:  "R1",
                    whitelist:  null,
                },
            ],
        },
    },
    sample_id                  = "cellranger-Aiptasia-apo_rep1",
    barcode_index              = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u7b8fcf6849/files/barcode_index.bi.bincode",
    barcode_correction_summary = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u7b8fcf67fa/files/summary.json",
)
